Little is known about the importance of landscape and land cover to the implementation and performance of agricultural conservation projects designed to improve stream quality. In our study, we addressed the potential importance of landscape and land cover to conservation projects by measuring variation across 191 μ-basins (100–2400 ha) and integrating the observed variation into a study design aimed at determining the effectiveness of conservation projects. Our findings indicate that there are strong gradients across which landscape and land cover attributes vary. Land cover varied along a gradient of agricultural intensity, basin morphometry across gradients of stream closure and basin size, basin substrate was described by variation in drumlin formation, glacial landform type, and soil drainage, while agricultural conservation projects varied according to the level of project implementation. Correlation of these gradients found several associations between landscape and land cover, indicating that agricultural intensity was being constrained predominantly by drumlin formation and glacial landform type. Landscape and land cover did not appear to be determining factors in the implementation of conservation projects by land owners. Based on these findings we chose 32 μ-basins which represented the variability along each of the defined gradients for further study. We conclude that landscape scale variables demonstrate important variation and covariation that can and should be integrated into study designs for the assessment of streams and human activities affecting streams.